A quick bit of background: For decades, health officials and advocates have been concerned about the overuse of antibiotics. The more you use an antibiotic, the more quickly bacteria resistant to it will emerge — and, indeed, the rise of resistant infections has far outpaced the development of new antibiotics to treat them.

Researchers have been focusing on extra-intestinal pathogenic E.coli, or ExPEC, a subset of E. coli strains that live in the gut and can cause infection in other body parts, like the urinary tract. McKenna writes:

ExPECs were already a medical-research concern, because E. coli that moves from the gut into the bladder may not stay there. Infections that are not treated can climb up to the kidneys and enter the bloodstream. ExPEC E. coli cause up to 40,000 deaths from sepsis — the most serious form of bloodborne bacterial infection — in the United States each year, and since about 2000, antibiotic resistance in ExPEC strains has been climbing.

In 2005, University of Minnesota professor of medicine Dr. James R. Johnson published results of two projects in which he analyzed meat bought in local supermarkets during 1999-2000 and 2001-2003. In both cases, he found resistant ExPEC E. coli strains that matched ones from human E. coli infections. Other researchers soon found similar matches in meat–particularly poultry–from across Europe, in Canada, and in additional studies from Minnesota and Wisconsin.

In that research, investigators began to sort out two things. They became convinced that the resistance pattern could be traced back to animal antibiotic use, because resistance genes in the bacteria causing human infections matched genes found in bacteria on conventionally raised meat. And they began to understand that E. coli’s complexity would make this new resistance problem a difficult one to solve. The strains that cross to humans via poultry meat “don’t establish themselves as big, successful lineages” of bacteria that would be easy to target, Johnson said. “But collectively they can cause a lot of infections, because there are just so many of them and they’re so diverse.”

There has been no way, to this point, to prove that a single specific UTI arose from a portion of meat that in turn came from a single animal given antibiotics. The investigators tracing the connection acknowledge this is a weakness in their case, but point out that modern medical ethics do not permit experimenters to deliberately cause infections in healthy humans as a way to prove a disease risk. What researchers do, in cases like this, is to gather evidence from big groups of people that shows a disease emerging on a population level — and based on the molecular evidence from animals, meat, and humans, they believe they have done so with ExPEC E.coli from chicken and UTIs.

McKenna does quote sources who point out that antibiotic resistance might be going from humans to livestock and back to humans, so we can’t assume antibiotic-dosed chickens are the original source of the problem. That misses the point, though: Livestock producers’ extensive use of antibiotics contributes to the emergence of antibiotic-resistant bacteria, so they should cut back — especially on the use of drugs that are also important for treating disease in humans.

Producers may disput the oft-cited estimate (which McKenna walks through here) that 80% of antibiotics sold in the US are given to livestock, but that doesn’t change the fact that according to FDA’s analysis, 28.8 million pounds of antibiotics were sold for use in food animals in 2009. We don’t know how much was used to treat disease in animals vs. to promote growth, but growth promotion is a common reason why livestock get the drugs. And while faster-growing animals may mean cheaper prices in the supermarket, I’d much rather spend a little more on animal products (or eat beans) than run the risk of contracting a once-benign infection that can no longer be treated effectively.